verhaar.rules

Class Rule21

java.lang.Object

java.util.Observable

toxTree.tree.AbstractRule

toxTree.tree.AbstractRuleHilightHits

toxTree.tree.rules.RuleSubstructures

toxTree.tree.rules.RuleRings

toxTree.tree.rules.RuleRingSubstituents

toxTree.tree.rules.RuleRingAllowedSubstituents

verhaar.rules.RuleRingMainStrucSubstituents

verhaar.rules.Rule21

All Implemented Interfaces:

Serializable, Cloneable, IDecisionRule, IImplementationDetails, IRuleSubstructures, XMLSerializable, IAlertCounter

Direct Known Subclasses:

Rule22, Rule23, Rule25

public class Rule21
extends RuleRingMainStrucSubstituents
implements IAlertCounter

Non- or weakly acidic phenols.

Author:

Nina Jeliazkova jeliazkova.nina@gmail.com Modified July 12, 2011

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected IAlertCounter	alertsCounter
protected ArrayList<String>	halogenIDs
protected String[]	halogens
protected int	halogensCount
protected int	maxHalogens
protected int	maxNitroGroups
protected int	nitroGroupsCount
protected ArrayList<String>	nitroIDs
protected ArrayList<String>	phenolIDs

Fields inherited from class verhaar.rules.RuleRingMainStrucSubstituents

mainStructure

Fields inherited from class toxTree.tree.rules.RuleRingSubstituents

analyzeOnlyRingsWithFlagSet, CONDITION_FAILED, CYCLIC_SUBSTITUENT, ERR_PRECONDITION_FAILED, LONGCHAIN_SUBSTITUENT

Fields inherited from class toxTree.tree.rules.RuleSubstructures

ids, MSG_HASGROUP

Fields inherited from class toxTree.tree.AbstractRule

changes, editable, ERR_STRUCTURENOTPREPROCESSED, examples, explanation, id, logger, MSG_NO, MSG_YES, no, residueIDHidden, title

Fields inherited from interface toxTree.core.XMLSerializable

xmltag_CATEGORIES, xmltag_CATEGORY, xmltag_CATEGORYTHRESHOLD, xmltag_CLASS, xmltag_EXPLANATION, xmltag_ID, xmltag_METHOD, xmltag_METHODPARAMETER, xmltag_METHODS, xmltag_NAME, xmltag_RULE, xmltag_RULEEXAMPLE, xmltag_RULES, xmltag_TREEROOT

Constructor Summary

Constructors

Constructor and Description
Rule21()

Method Summary

Modifier and Type	Method and Description
protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer	createMainStructure()
protected String[]	getHalogens()
String	getImplementationDetails()
int	getMaxHalogens()
int	getMaxNitroGroups()
void	incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)
protected QueryAtomContainers	initQuery()
boolean	isImplemented()
void	setMaxHalogens(int maxHalogens)
void	setMaxNitroGroups(int maxNitroGroups)
boolean	substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a, int[] place) returns true if the substituent is allowed and false if it is forbidden to be implemented by the inheriting class
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol) IDecisionRule.verifyRule(IAtomContainer)
boolean	verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol, org.openscience.cdk.interfaces.IAtomContainer selected) returns true if only allowed substituents are found

Methods inherited from class toxTree.tree.rules.RuleRingSubstituents

allowedSubstituents, analyze, analyzeOnlyRingsWithFlagSet, clearFlags, getFlag, setAnalyzeAromatic, setAnalyzeHeterocyclic, setAnalyzeOnlyRingsWithFlagSet, setFlag

Methods inherited from class toxTree.tree.rules.RuleRings

hasRingsToProcess

Methods inherited from class toxTree.tree.rules.RuleSubstructures

addSubstructure, clearSubstructures, equals, getIds, getQuery, getSubstructure, getSubstructures, getSubstructuresCount, removeSubstructure, setIds, setQuery, setSubstructure

Methods inherited from class toxTree.tree.AbstractRuleHilightHits

getSelector

Methods inherited from class toxTree.tree.AbstractRule

addPropertyChangeListener, clearFlags, clone, createRule, fromXML, getEditor, getExampleMolecule, getExamples, getExplanation, getID, getNum, getTitle, hideResiduesID, isEditable, isResidueIDHidden, log, log, log, makeMolecule, removePropertyChangeListener, setEditable, setExampleMolecule, setExamples, setExplanation, setID, setNum, setTitle, toShallowXML, toString, toXML

Methods inherited from class java.util.Observable

addObserver, clearChanged, countObservers, deleteObserver, deleteObservers, hasChanged, notifyObservers, notifyObservers, setChanged

Methods inherited from class java.lang.Object

finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface toxTree.core.IDecisionRule

addPropertyChangeListener, clearFlags, clone, getEditor, getExampleMolecule, getExplanation, getID, getNum, getSelector, getTitle, hideResiduesID, isEditable, isResidueIDHidden, removePropertyChangeListener, setEditable, setExampleMolecule, setExplanation, setID, setNum, setTitle, toString

Field Detail

alertsCounter

protected IAlertCounter alertsCounter

nitroGroupsCount

protected transient int nitroGroupsCount

halogensCount

protected transient int halogensCount

halogens

protected transient String[] halogens

nitroIDs

protected ArrayList<String> nitroIDs

phenolIDs

protected ArrayList<String> phenolIDs

halogenIDs

protected ArrayList<String> halogenIDs

maxHalogens

protected int maxHalogens

maxNitroGroups

protected int maxNitroGroups

Constructor Detail

Rule21

public Rule21()
       throws Exception

Throws:

Exception

Method Detail

initQuery

protected QueryAtomContainers initQuery()
                                 throws Exception

Overrides:

initQuery in class RuleRingMainStrucSubstituents

Throws:

Exception

getHalogens

protected String[] getHalogens()

createMainStructure

protected org.openscience.cdk.isomorphism.matchers.QueryAtomContainer createMainStructure()
                                                                                   throws org.openscience.cdk.exception.CDKException

Specified by:

createMainStructure in class RuleRingMainStrucSubstituents

Throws:

org.openscience.cdk.exception.CDKException

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol)
                   throws DecisionMethodException

Description copied from class: RuleRingSubstituents

IDecisionRule.verifyRule(IAtomContainer)

Specified by:

verifyRule in interface IDecisionRule

Overrides:

verifyRule in class RuleRingAllowedSubstituents

Parameters:

mol - org.openscience.cdk.interfaces.AtomContainer

Returns:

rule result, boolean

Throws:

DecisionMethodException

verifyRule

public boolean verifyRule(org.openscience.cdk.interfaces.IAtomContainer mol,
                          org.openscience.cdk.interfaces.IAtomContainer selected)
                   throws DecisionMethodException

Description copied from class: RuleRingAllowedSubstituents

returns true if only allowed substituents are found

Overrides:

verifyRule in class RuleRingAllowedSubstituents

Throws:

DecisionMethodException

substituentIsAllowed

public boolean substituentIsAllowed(org.openscience.cdk.interfaces.IAtomContainer a,
                                    int[] place)
                             throws DecisionMethodException

Description copied from class: RuleRingSubstituents

returns true if the substituent is allowed and false if it is forbidden to be implemented by the inheriting class

Overrides:

substituentIsAllowed in class RuleRingAllowedSubstituents

Throws:

DecisionMethodException

isImplemented

public boolean isImplemented()

Specified by:

isImplemented in interface IDecisionRule

Overrides:

isImplemented in class RuleRingAllowedSubstituents

Returns:

false if the rule is not implemented and true if it is

getMaxHalogens

public int getMaxHalogens()

setMaxHalogens

public void setMaxHalogens(int maxHalogens)

getMaxNitroGroups

public int getMaxNitroGroups()

setMaxNitroGroups

public void setMaxNitroGroups(int maxNitroGroups)

getImplementationDetails

public String getImplementationDetails()

Specified by:

getImplementationDetails in interface IImplementationDetails

incrementCounter

public void incrementCounter(org.openscience.cdk.interfaces.IAtomContainer mol)

Specified by:

incrementCounter in interface IAlertCounter